Operating systems are pirated more and more often. Apple doesn't expect a huge increase in software sales if they open it up to all machines, they see a piracy increase (as well as an increase in OTHER companies hardware).
Much like iTunes' purpose is to sell iPods and iPhones, Mac OS X is for selling Macs.
Apple's cheapest notebook is $999, much more expensive than a $299 netbook. They don't want that type of competition.